It dawned on me that the gray current shifting and flickering below the surface of Raceway 5 was actually hundreds of thousands of three-inch-long fall-run chinooks. A hatchery worker scooped up a couple: squiggles with woeful expressions, they were barely princelings, never mind kings. But every so often one would snap itself suddenly out of the big pond, a hint of the athleticism that would one day launch it upstream.

We were there because the hatchery was taking a historic step. Usually, the federal facility—at the northern end of California's Central Valley—releases the juveniles out its back door into Battle Creek, which feeds into the Sacramento River six miles downstream. This year, though, natural resource managers had decided to load 1.4 million fish, about a tenth of Coleman's total stock, into trucks and drive them roughly 200 miles south to San Pablo Bay, above San Francisco Bay, bypassing the entire river, a tactic that state hatcheries have been using for years. I had already been startled to learn that between 50 percent and 90 percent of the Sacramento River's "wild" fall-run chinooks are actually born in hatcheries, which were created to compensate for the loss of spawning grounds to dams. Every autumn, hatchery workers trap returning adults before they spawn and strip them of sperm and eggs. The offspring are incubated in trays and fed pellets. Now this latest batch would not even have to swim down the river.

The shipment was an effort to rekindle future fishing seasons, Scott Hamelberg, the hatchery manager, said: "If you truck a fish from Coleman and bypass certain areas where mortality can happen, you may improve survival. You take out hundreds of miles of avoiding predators, water diversions, pollution, any number of things."

We spoke in his office, which held a shrine to Popeye, a cat who must have enjoyed an extremely happy tenure at the hatchery. Despite the low numbers of returning Sacramento salmon this year, Coleman planned to go ahead with its annual Return of the Salmon Festival in the third week of October, where in years past schoolchildren have shrieked over the chinooks jamming the creek.

Outside, a worker standing waist-deep in the raceway crowded the fish toward a hydraulic pump, using a broom to goad stragglers. Their shadowy forms shot up a transparent tube and into a tank on a waiting truck. In a few hours they would be piped into net pens in the bay, then hauled by boat farther out and released to swim out to sea. Some scientists say the hatchery fish are less physically fit than their wild brethren, with a swimming-pool mentality that does not serve them well in the ocean. And yet in years past, many survived to maturity simply because they were introduced in such overwhelming numbers. Some wildlife experts speculate that the hatchery-born fish may even be weakening wild populations they were meant to bolster by competing with the river-born fish for food and space, and heading home with them to breed, altering the gene pool.

The trucked fish won't know where home is, exactly. Many will likely never find their way back to Battle Creek, not having swum down the river in the first place. These strays might spawn successfully elsewhere, but without that initial migration it might seem that some essential quality of salmon-ness is lost.

If this is the price of keeping the species going, so be it, said Hamelberg, who wears a wedding band etched with tiny salmon. "There's a greater public good here," he told me. "We're providing fish to the American public to eat, and also for aesthetic reasons—just for people to know they're in the system, that they returned. Our obligation is to keep these runs as sound as possible."

The hatchery workers looked weary as the trucks pulled away. As it turns out, chauffeuring tons of pinkie-length fish hundreds of miles is trickier than it sounds. During shipping the day before, the circulation system in one of the trucks stopped working, and 75,000 chinooks died.

Native peoples of the Pacific Northwest used to think salmon were immortal, and it's easy to see why. Even though the rivers hosted spectacular mass death scenes every year and were filled for weeks with rotting bodies, the next season's fish always mobbed the gravel beds. To safeguard this cycle, tribes were careful to place the bones of the season's first catch back in the river.

But the California and Pacific Northwest salmon populations have been declining for more than a century and a half. Gold miners washed the gravel out of streams and loggers dismembered river habitats. Fishermen caught so many salmon that the canneries couldn't keep up; barge loads were dumped back into the sea, and salmon carcasses were used to feed hogs and fertilize fields. Today, the Columbia River supports at most 3 percent of the salmon it boasted when Lewis and Clark passed through. The Klamath River, which starts in southern Oregon, has suffered major salmon kills. Some Pacific salmon varieties may share the fate of their East Coast cousins, the wild Atlantic salmon, which were killed off in huge numbers in the 19th century by overfishing, pollution and dams and are today nearly extinct in the wild.

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